# HG changeset patch
# User artbio
# Date 1504350551 14400
# Node ID d76a0d8a9eace477d788e56e1888ac4fc54a4ac2

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a

diff -r 000000000000 -r d76a0d8a9eac cap3.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cap3.xml	Sat Sep 02 07:09:11 2017 -0400
@@ -0,0 +1,91 @@
+<tool id="cap3" name="cap3" version="2.0.0">
+<description>Sequence Assembly tool</description>
+    <requirements>
+    	<requirement type="package" version="10.2011">cap3</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Tool exception" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+    cap3 "$inputSequences" -o $overlaplength -p $overlapidentity > "$cap3stdout" &&
+                mv "$inputSequences".cap.contigs $contigs &&
+                mv "$inputSequences".cap.contigs.qual $contigsqual &&
+                mv "$inputSequences".cap.contigs.links $contigslink &&
+                mv "$inputSequences".cap.ace $ace &&
+                mv "$inputSequences".cap.info $info &&
+                mv "$inputSequences".cap.singlets $singlets &&
+                cat $contigs $singlets > $contigsandsinglets
+    ]]></command>
+
+        <inputs>
+        	<param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" />
+        	<param label="specify overlap length cutoff > 15 (40)" name="overlaplength" type="integer" size="3" value="40" help="-o option. must be > 15. 40 by default" />
+        	<param label="specify overlap percent identity cutoff N > 65 (90)" name="overlapidentity" type="integer" size="3" value="90"  help="-p option. must be > 65. 90 by default" />
+        </inputs>
+
+<outputs>
+                <data format="fasta" name="contigsandsinglets" label="${tool.name} on ${on_string}: Contigs and singlets" from_work_dir="${inputSequences}.cap.contigs" />
+        	    <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output" hidden="true"/>
+                <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" />
+                <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="true" />
+                <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="true" />
+                <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="true" />
+                <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="true" />
+                <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" />
+</outputs>
+
+  <tests>
+    <test>
+      <param name="inputSequences" value="input.fa" ftype="fasta"/>
+      <param name="overlaplength" value="40" />
+      <param name="overlapidentity" value="90" />
+      <output name="contigsandsinglets" file="contigsandsinglets.fa"/>
+      <output name="cap3stdout" file="cap3stdout.txt"/>
+      <output name="contigs" file="contigs.fa"/>
+      <output name="contigsqual" file="contigsqual.txt"/>
+      <output name="contigslink" file="contigslink.txt"/>
+      <output name="ace" file="ace.txt"/>
+      <output name="info" file="info.txt"/>
+      <output name="singlets" file="singlets.fa"/>
+    </test>
+  </tests>
+
+
+<help>
+**What it does**
+
+This tool is a CAP3 wrapper developed for the visitor2 set of worflows
+
+Under this conditions, it takes as input a set of blast hits in fasta format and performs CAP3 assembly on these sequences
+
+Standard CAP3 outputs (Standard Output, Contigs Qual, Contigs Link, Ace and Info) are kept hidden in the Galaxy history (feel free to reveal these hidden datasets).
+
+Standard CAP3 outputs Contigs and Singlets are returned in the history, as well as a merge of these two datasets (Contigs and singlets)
+
+**Acknowledgments**
+
+This Galaxy tool makes use of the `package_cap3_3`_ Galaxy package developed by jjohnson.
+
+It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
+
+.. _package_cap3_3: https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_cap3_3
+.. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
+.. _MIT license: http://opensource.org/licenses/MIT
+
+
+</help>
+  <citations>
+      <citation type="bibtex">@article{Huang:1999wb,
+       author = {Huang, X and Madan, A},
+       title = {{CAP3: A DNA sequence assembly program.}},
+       journal = {Genome research},
+       year = {1999},
+       volume = {9},
+       number = {9},
+      pages = {868--877},
+      month = sep
+      }
+      </citation>
+  </citations>
+  
+</tool>
diff -r 000000000000 -r d76a0d8a9eac test-data/ace.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ace.txt	Sat Sep 02 07:09:11 2017 -0400
@@ -0,0 +1,296 @@
+AS 4 13
+
+CO Contig1 1372 7 2 U
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
+CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
+TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
+TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
+CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
+ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
+CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
+TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
+TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
+TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
+GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
+GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
+TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
+TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
+AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
+AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
+TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
+
+BQ
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 25 25 25 25 25 25 25 25 25 
+25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 25 25 25 25 25 25 25 25 25 25 
+25 25 25 25 25 25 25 25 10 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_1/7_Confidence_0.286_Length_199_hit1_IdMatch=98.48,AligLength=197,E-val=2e-92 U 1
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_3/7_Confidence_0.286_Length_395_hit1_IdMatch=97.97,AligLength=395,E-val=0.0 U 1
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_2/7_Confidence_0.143_Length_224_hit1_IdMatch=97.77,AligLength=224,E-val=3e-104 U 172
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_4/7_Confidence_0.286_Length_409_hit1_IdMatch=96.58,AligLength=409,E-val=0.0 U 370
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_5/7_Confidence_0.286_Length_421_hit1_IdMatch=96.67,AligLength=421,E-val=0.0 U 351
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_6/7_Confidence_0.143_Length_1372_hit1_IdMatch=97.59,AligLength=1372,E-val=0.0 U 1
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_7/7_Confidence_0.000_Length_627_hit1_IdMatch=97.93,AligLength=627,E-val=0.0 U 746
+BS 1 395 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_3/7_Confidence_0.286_Length_395_hit1_IdMatch=97.97,AligLength=395,E-val=0.0
+BS 396 1372 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_6/7_Confidence_0.143_Length_1372_hit1_IdMatch=97.59,AligLength=1372,E-val=0.0
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_1/7_Confidence_0.286_Length_199_hit1_IdMatch=98.48,AligLength=197,E-val=2e-92 197 0 0
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGC
+
+QA 1 197 1 197
+DS 
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_3/7_Confidence_0.286_Length_395_hit1_IdMatch=97.97,AligLength=395,E-val=0.0 395 0 0
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC
+
+QA 1 395 1 395
+DS 
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_2/7_Confidence_0.143_Length_224_hit1_IdMatch=97.77,AligLength=224,E-val=3e-104 224 0 0
+ACATCCTGGGTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTT
+GGCCGTACCTCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGG
+ACATATGCCATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGAT
+ACTCCTGCAACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC
+
+QA 1 224 1 224
+DS 
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_4/7_Confidence_0.286_Length_409_hit1_IdMatch=96.58,AligLength=409,E-val=0.0 409 0 0
+TTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTTCTGGCTGCA
+GTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTGTCCTGCAAT
+GTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCATCTCCAGTA
+GTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCTCCAACTTTA
+TCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTAACGACGGCT
+TGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATCCGAACTACT
+TTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGT
+TTAAGAG
+
+QA 1 402 1 402
+DS 
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_5/7_Confidence_0.286_Length_421_hit1_IdMatch=96.67,AligLength=421,E-val=0.0 421 0 0
+TACTCCTGCAACGTCCAGATTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAA
+AGCTGACGTTCTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTC
+TCTTTGACTGTCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTC
+TCCAAGTTCATCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTA
+GGCACTAGCTCCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGT
+AAGCCATCTAACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACT
+TTCTGTGATCCGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGG
+T
+
+QA 1 421 1 421
+DS 
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_6/7_Confidence_0.143_Length_1372_hit1_IdMatch=97.59,AligLength=1372,E-val=0.0 1372 0 0
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
+CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
+TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
+TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
+CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
+ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
+CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
+TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
+TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
+TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
+GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
+GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
+TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
+TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
+AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
+AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
+TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
+
+QA 1 1372 1 1372
+DS 
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_7/7_Confidence_0.000_Length_627_hit1_IdMatch=97.93,AligLength=627,E-val=0.0 627 0 0
+GTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCCTCAAACACTTTGTACTCATCATTCA
+GATTCGCCTCAGGAGGAGGAGGGCATCCTACAACCTCCTTGACATCATAGTCGTTGGATT
+GGACTGTCAAATTTATCTGCCTCACAGCCACTCTCTGCTCCCTCTTAAACTCGTCCAGGA
+ATCCTGACAATGTGGGGAACAGATTAATCCATCCCGCTTTGTCATCCTCTCCATCTGAAT
+AGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCTGACGAATCTGGATATTCAAAGTCCT
+GGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGCTCTTGCGTTTGCATGACAATAATCT
+CGCCGGGGATTGTGTTAACCACAGCGTGTATTGTCTCTTCGATCCGAGGTATGCTGAATC
+CCATTGTTATCATTAAACCCCTCATACGGTCATACAGAGTTCTTTGGCGTGCCGTTCTAG
+ATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAGAGCATCATCTCAAGAGCATCGCTCT
+CAGGCATTGTGGGGACATGTATCACACGGTGTCTGTGGTACACTCCCATAATTTGTACGC
+CAAGAAATTTGTGGTCCGTAATTAGAC
+
+QA 1 627 1 627
+DS 
+
+CO Contig2 515 2 3 U
+TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+GATGAAGAGACAAGGCTTAGTTGTCAAAGAGGGAA
+
+BQ
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 0 15 15 15 15 15 15 15 10 10 10 10 10 10 10 10 10 
+
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_2/2_Confidence_0.333_Length_515_hit1_IdMatch=97.28,AligLength=515,E-val=0.0 U 1
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_1/2_Confidence_0.667_Length_506_hit1_IdMatch=97.04,AligLength=506,E-val=0.0 U 1
+BS 1 498 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_2/2_Confidence_0.333_Length_515_hit1_IdMatch=97.28,AligLength=515,E-val=0.0
+BS 499 499 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_1/2_Confidence_0.667_Length_506_hit1_IdMatch=97.04,AligLength=506,E-val=0.0
+BS 500 515 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_2/2_Confidence_0.333_Length_515_hit1_IdMatch=97.28,AligLength=515,E-val=0.0
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_2/2_Confidence_0.333_Length_515_hit1_IdMatch=97.28,AligLength=515,E-val=0.0 515 0 0
+TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+GATGAAGAGACAAGGCTTGGTTGTCAAAGAGGGAA
+
+QA 1 515 1 515
+DS 
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_1/2_Confidence_0.667_Length_506_hit1_IdMatch=97.04,AligLength=506,E-val=0.0 506 0 0
+TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+GATGAAGAGACAAGGCTTAGTTGTCA
+
+QA 1 506 1 506
+DS 
+
+CO Contig3 284 2 3 U
+AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG
+TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
+AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
+AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
+TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+
+BQ
+10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 0 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_2/2_Confidence_0.000_Length_284_hit1_IdMatch=98.94,AligLength=284,E-val=2e-139 U 1
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_1/2_Confidence_0.667_Length_236_hit1_IdMatch=98.73,AligLength=236,E-val=2e-113 U 49
+BS 1 73 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_2/2_Confidence_0.000_Length_284_hit1_IdMatch=98.94,AligLength=284,E-val=2e-139
+BS 74 74 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_1/2_Confidence_0.667_Length_236_hit1_IdMatch=98.73,AligLength=236,E-val=2e-113
+BS 75 284 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_2/2_Confidence_0.000_Length_284_hit1_IdMatch=98.94,AligLength=284,E-val=2e-139
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_2/2_Confidence_0.000_Length_284_hit1_IdMatch=98.94,AligLength=284,E-val=2e-139 284 0 0
+AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG
+TGAATCAGGTTTATGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
+AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
+AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
+TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+
+QA 1 284 1 284
+DS 
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_1/2_Confidence_0.667_Length_236_hit1_IdMatch=98.73,AligLength=236,E-val=2e-113 236 0 0
+ATAGAAGCACTGTGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTG
+CCTATCTCCAGGAGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTC
+TCCATGAGTCGGAAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTG
+ACACTAAGAAAGTTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+
+QA 1 236 1 236
+DS 
+
+CO Contig4 253 2 1 U
+TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
+CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
+ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
+GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
+ACAGTTCTTGTTA
+
+BQ
+10 10 10 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 
+
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_1/2_Confidence_0.667_Length_253_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118 U 1
+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_2/2_Confidence_0.333_Length_251_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118 U 3
+BS 1 253 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_1/2_Confidence_0.667_Length_253_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_1/2_Confidence_0.667_Length_253_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118 253 0 0
+TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
+CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
+ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
+GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
+ACAGTTCTTGTTA
+
+QA 1 253 1 253
+DS 
+
+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_2/2_Confidence_0.333_Length_251_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118 251 0 0
+T
+GGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCACCG
+AGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACAATT
+TCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTCGTT
+CCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCAACA
+GTTCTTGTTA
+
+QA 2 251 2 251
+DS 
+
diff -r 000000000000 -r d76a0d8a9eac test-data/cap3stdout.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cap3stdout.txt	Sat Sep 02 07:09:11 2017 -0400
@@ -0,0 +1,299 @@
+Number of segment pairs = 342; number of pairwise comparisons = 14
+'+' means given segment; '-' means reverse complement
+
+Overlaps            Containments  No. of Constraints Supporting Overlap
+
+******************* Contig 1 ********************
+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+                    gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+ is in gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+                    gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+ is in gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+                    gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+ is in gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+                    gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+ is in gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+******************* Contig 2 ********************
+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+                    gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+ is in gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+******************* Contig 3 ********************
+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+******************* Contig 4 ********************
+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+
+
+DETAILED DISPLAY OF CONTIGS
+******************* Contig 1 ********************
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+gi|225356593|gb|FJ15+ GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+gi|225356593|gb|FJ15+ GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+                      ____________________________________________________________
+consensus             GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+gi|225356593|gb|FJ15+ GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+gi|225356593|gb|FJ15+ GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+                      ____________________________________________________________
+consensus             GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+gi|225356593|gb|FJ15+ TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+gi|225356593|gb|FJ15+                                                    ACATCCTGG
+gi|225356593|gb|FJ15+ TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+                      ____________________________________________________________
+consensus             TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+gi|225356593|gb|FJ15+ GTATGGTGGCTGTGGGC                                           
+gi|225356593|gb|FJ15+ GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+gi|225356593|gb|FJ15+ GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+                      ____________________________________________________________
+consensus             GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+gi|225356593|gb|FJ15+ TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+gi|225356593|gb|FJ15+ TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+                      ____________________________________________________________
+consensus             TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+gi|225356593|gb|FJ15+ ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+gi|225356593|gb|FJ15+ ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+gi|225356593|gb|FJ15+                                                   TACTCCTGCA
+                      ____________________________________________________________
+consensus             ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC                         
+gi|225356593|gb|FJ15+ ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC                         
+gi|225356593|gb|FJ15+ ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
+gi|225356593|gb|FJ15+          TTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
+gi|225356593|gb|FJ15+ ACGTCCAGATTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
+                      ____________________________________________________________
+consensus             ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
+gi|225356593|gb|FJ15+ CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
+gi|225356593|gb|FJ15+ CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
+                      ____________________________________________________________
+consensus             CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
+gi|225356593|gb|FJ15+ TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
+gi|225356593|gb|FJ15+ TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
+                      ____________________________________________________________
+consensus             TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
+gi|225356593|gb|FJ15+ TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
+gi|225356593|gb|FJ15+ TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
+                      ____________________________________________________________
+consensus             TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
+gi|225356593|gb|FJ15+ CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
+gi|225356593|gb|FJ15+ CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
+                      ____________________________________________________________
+consensus             CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
+gi|225356593|gb|FJ15+ ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
+gi|225356593|gb|FJ15+ ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
+                      ____________________________________________________________
+consensus             ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
+gi|225356593|gb|FJ15+ CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGT         
+gi|225356593|gb|FJ15+ CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGT         
+gi|225356593|gb|FJ15+                          GTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
+                      ____________________________________________________________
+consensus             CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
+gi|225356593|gb|FJ15+ TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
+                      ____________________________________________________________
+consensus             TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
+gi|225356593|gb|FJ15+ TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
+                      ____________________________________________________________
+consensus             TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
+gi|225356593|gb|FJ15+ TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
+                      ____________________________________________________________
+consensus             TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
+gi|225356593|gb|FJ15+ GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
+                      ____________________________________________________________
+consensus             GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
+gi|225356593|gb|FJ15+ GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
+                      ____________________________________________________________
+consensus             GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
+gi|225356593|gb|FJ15+ TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
+                      ____________________________________________________________
+consensus             TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
+gi|225356593|gb|FJ15+ TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
+                      ____________________________________________________________
+consensus             TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
+gi|225356593|gb|FJ15+ AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
+                      ____________________________________________________________
+consensus             AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
+gi|225356593|gb|FJ15+ AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
+                      ____________________________________________________________
+consensus             AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
+gi|225356593|gb|FJ15+ TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
+                      ____________________________________________________________
+consensus             TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
+
+******************* Contig 2 ********************
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+gi|225356593|gb|FJ15+ TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+                      ____________________________________________________________
+consensus             TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+gi|225356593|gb|FJ15+ AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+                      ____________________________________________________________
+consensus             AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+gi|225356593|gb|FJ15+ GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+                      ____________________________________________________________
+consensus             GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+gi|225356593|gb|FJ15+ GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+                      ____________________________________________________________
+consensus             GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+gi|225356593|gb|FJ15+ GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+                      ____________________________________________________________
+consensus             GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+gi|225356593|gb|FJ15+ CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+                      ____________________________________________________________
+consensus             CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+gi|225356593|gb|FJ15+ TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+                      ____________________________________________________________
+consensus             TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+gi|225356593|gb|FJ15+ GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+                      ____________________________________________________________
+consensus             GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GATGAAGAGACAAGGCTTGGTTGTCAAAGAGGGAA
+gi|225356593|gb|FJ15+ GATGAAGAGACAAGGCTTAGTTGTCA         
+                      ____________________________________________________________
+consensus             GATGAAGAGACAAGGCTTAGTTGTCAAAGAGGGAA
+
+******************* Contig 3 ********************
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG
+gi|225356593|gb|FJ15+                                                 ATAGAAGCACTG
+                      ____________________________________________________________
+consensus             AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TGAATCAGGTTTATGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
+gi|225356593|gb|FJ15+ TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
+                      ____________________________________________________________
+consensus             TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
+gi|225356593|gb|FJ15+ AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
+                      ____________________________________________________________
+consensus             AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
+gi|225356593|gb|FJ15+ AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
+                      ____________________________________________________________
+consensus             AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+gi|225356593|gb|FJ15+ TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+                      ____________________________________________________________
+consensus             TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+
+******************* Contig 4 ********************
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
+gi|225356593|gb|FJ15+    GGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
+                      ____________________________________________________________
+consensus             TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
+gi|225356593|gb|FJ15+ CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
+                      ____________________________________________________________
+consensus             CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
+gi|225356593|gb|FJ15+ ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
+                      ____________________________________________________________
+consensus             ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
+gi|225356593|gb|FJ15+ GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
+                      ____________________________________________________________
+consensus             GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
+
+                          .    :    .    :    .    :    .    :    .    :    .    :
+gi|225356593|gb|FJ15+ ACAGTTCTTGTTA
+gi|225356593|gb|FJ15+ ACAGTTCTTGTTA
+                      ____________________________________________________________
+consensus             ACAGTTCTTGTTA
+
diff -r 000000000000 -r d76a0d8a9eac test-data/contigs.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.fa	Sat Sep 02 07:09:11 2017 -0400
@@ -0,0 +1,46 @@
+>Contig1
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
+CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
+TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
+TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
+CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
+ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
+CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
+TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
+TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
+TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
+GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
+GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
+TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
+TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
+AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
+AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
+TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
+>Contig2
+TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+GATGAAGAGACAAGGCTTAGTTGTCAAAGAGGGAA
+>Contig3
+AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG
+TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
+AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
+AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
+TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+>Contig4
+TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
+CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
+ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
+GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
+ACAGTTCTTGTTA
diff -r 000000000000 -r d76a0d8a9eac test-data/contigsandsinglets.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigsandsinglets.fa	Sat Sep 02 07:09:11 2017 -0400
@@ -0,0 +1,91 @@
+>Contig1
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
+CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
+TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
+TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
+CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
+ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
+CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
+TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
+TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
+TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
+GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
+GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
+TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
+TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
+AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
+AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
+TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
+>Contig2
+TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+GATGAAGAGACAAGGCTTAGTTGTCAAAGAGGGAA
+>Contig3
+AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG
+TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
+AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
+AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
+TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+>Contig4
+TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
+CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
+ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
+GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
+ACAGTTCTTGTTA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_29_Transcript_1/1_Confidence_0.000_Length_607_hit1_IdMatch=97.7,AligLength=608,E-val=0.0
+ACGCCCGAGAGCGTGGTCTTGGGCATGGCACTGTAGGCGACCTGACTCCCAGACTTTCGA
+GGGCGATTTCGCCCTCTTCGACGGGGTCCTTGAACCATTGAGCAATTCTTTCCCACAATT
+TGACGAGAAGATACACTCTGTACGGTAACCTTGGGGGAACGACGGTTTCTGGTGGAAAGA
+TTGTTTCCACTGTTGTTTGATATGCGCTTTGTAGTTGTGACGATGGTGGCCATGGCATAA
+TATTTACAAATTGTATTCTTGATTTGAGTTTGGGTTGTTTGATGTTATAGGGTCGGCAAG
+AGCTTACTTGCAGTTCTCTTCCTCTTTTTGCGGTCGAGAGTCTTTTTGTTGAGTCTCGTC
+CTTTGTTCTGCGGTCAGCAGTGATCTCTTCGATGCTACTTTAGGAGGTGGAAACCGGGAG
+AATAAGTCTTGAATTCTCACACGGTAGTCATCAGGATTTTTATGACTAACCTCTCTAATA
+AGCATCTGCACCTGGCGGGGACAGTGCCCCGGGAATTGCTGCATTATACTGTGAAACAGC
+TCCAAATCCAGGGTTTCATGAACGGGCACAATCTGTGGCACAGCTTTAGGGGCAGTTGCA
+TATTCAA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_27_Transcript_1/1_Confidence_0.000_Length_471_hit1_IdMatch=97.66,AligLength=471,E-val=0.0
+GCAAAAAGAATGCCTCTGATAGGGCAATCATAAAACTGTTAAACAAATACATGCCTAGGA
+CAGGAAATAAGAACTGGCCTGGTGTCCATACAACCCCGGAAGAAGGCATACTTGATGGTA
+TTAAGATAACGGCCAAATCCAGTGCAGGCGCTCCCTATTGGAGACACAAGGGGGAATGCC
+TAGACCATATAATTGATACTGGACTTCCTGTTGTGCTAAAGCATATAAAGGAAGGAACCC
+TCAATCAGTTGTGGCGGGAAAACCCTGAGATGTTCCTCGTTGAAGTTAAGAACAAACTTG
+ATAGATACGAGGTTTCGAAGCTTAAAGAGAAGACTAGACCCTATGTGTGTGTACCTGCGC
+ACTGGGCTCTCCTATTCTCGTGCTTGACTCAAGGATTCCAAGAAGGACTTCAAGTTTTTA
+GTAACTTGGACCCCAGTACAGAATGCTCGAATGCATATGGATTTTCATCCA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_14_Transcript_1/1_Confidence_0.000_Length_210_hit1_IdMatch=98.1,AligLength=210,E-val=3e-98
+TGTCCCGTTGCACCCCCCATCCATTAACAATCGGGGTGGGCATACTCATGTCACTCGCCA
+GATGGGCGGAGTACCTCACCCTCCTCTTGGTCTAATACCCATAGCTCAGAAGTACGGGGT
+AGAGATCTTGGACCAGAAACATGTCTACACAGGAGGCACTTGGGATGGCTTTCTTAATAG
+ACTCGCCCAACAGATGGGCCGGACAACGGT
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_24_Transcript_1/1_Confidence_0.000_Length_280_hit1_IdMatch=96.79,AligLength=280,E-val=4e-129
+ACCATTTGTCCCCCATGGTGCATTTTCATGGTAAGGTAGTCACTGTTCCAGGAACCATCT
+GAGGTGGTAAAAAGGTCCTGGAAACCAGTATCTGGAGTGATATCCTCGTCAATGGAGACA
+GCTCCTAATTCAGCACCTTCAAACTCAATCACCCATTCGAGTGTGACAGTGAAGGTGGTG
+CTTCCTGTGTATCCACCGGTGGTAGAGGCAACAACCACATTGATGAAGCCATGATTGGCG
+TCATCAGGGTTGCCTTTGGTGAGATACCACTTACGGGTGG
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_22_Transcript_1/1_Confidence_0.000_Length_289_hit1_IdMatch=95.5,AligLength=289,E-val=1e-128
+GGCCTGCAGGCCATAACTCGGTTGAGGTTTTGAGTGTCATTGCCTGAGATATTGTTGGCG
+GGGTCTGGAGACCATCCTATGGCAAGGGATCCAAAAGTATTTGCACTTCCAGATCCCACT
+ACCAGCACTCGGAGTTTCTTGGGTCGCCAGCGGGAATATAGCTTACTCTGCTGCTGAAGC
+CTAGAATCACTCATAGCCGTTGGACATATGGCTTGAGCAAAAAGGCTAGCTCCCACTGCG
+CGCTGCGGTTGTACCTCAATAACGCCTATAATGTCCACGCCCGAGAGCG
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_20_Transcript_1/1_Confidence_0.000_Length_352_hit1_IdMatch=98.01,AligLength=352,E-val=8e-171
+GCATTCACTGCTCTAAGTTGCTCGGTCAGCTGGTCAATGCGGCGAAGTAGATTAGTTTCG
+ACAGTCTGAACTGCTTCATCAGCCACCCTAAATTTAGGGATGGGAGGGCTAATGACAGGA
+CCTTGGGTGTAATACTTGAGACATTTGCCAGTATCTCCAGTGCGGATATAATCTTTTGCA
+TCTGTGTAACTGGCAAACATAACAAAACCTGGGATAGAGTAACCTTGTATAACTGCAAAG
+AAGTTTGCTGTCTTCAAGGTCGTCTTGTCCTCAAGGTAGTAGGTTACATTTGTCCCTGGT
+GCATTTGTATACACATAAGCCTGGTGGGCAGCCGAAAAGGGGACCATTTGTC
diff -r 000000000000 -r d76a0d8a9eac test-data/contigslink.txt
diff -r 000000000000 -r d76a0d8a9eac test-data/contigsqual.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigsqual.txt	Sat Sep 02 07:09:11 2017 -0400
@@ -0,0 +1,127 @@
+>Contig1
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 25 25 25 25 25 25 25 25 25 
+25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 25 25 25 25 25 25 25 25 25 25 
+25 25 25 25 25 25 25 25 10 30 30 30 30 30 30 30 30 30 30 30 
+30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 
+20 20 20 20 20 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 
+25 25 25 25 25 25 25 25 25 25 25 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 
+>Contig2
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 0 15 
+15 15 15 15 15 15 10 10 10 10 10 10 10 10 10 
+>Contig3
+10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 
+10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 
+10 10 10 10 10 10 10 10 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 0 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 
+>Contig4
+10 10 10 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 
+15 15 15 15 15 15 15 15 15 15 15 15 15 
diff -r 000000000000 -r d76a0d8a9eac test-data/info.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/info.txt	Sat Sep 02 07:09:11 2017 -0400
@@ -0,0 +1,23 @@
+No file of quality values (.qual) is found
+No file of constraints (.con) is found.
+Number of overlaps saved: 12
+ComputeOverlap done
+IdentifyChimeras done
+Number of overlaps removed: 0
+RemovePoorOverlaps done
+ASSEM done
+ComputDistForContigs done
+PresentLayout done
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 395,  length: 395,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 197,  length: 197,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 224,  length: 224,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 1372,  length: 1372,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 402,  length: 409,  right size 7
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 421,  length: 421,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 627,  length: 627,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 515,  length: 515,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 506,  length: 506,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 284,  length: 284,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 236,  length: 236,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 4, right clip: 253,  length: 253,  right size 0
+Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 2, right clip: 251,  length: 251,  right size 0
diff -r 000000000000 -r d76a0d8a9eac test-data/input.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fa	Sat Sep 02 07:09:11 2017 -0400
@@ -0,0 +1,159 @@
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_4/7_Confidence_0.286_Length_409_hit1_IdMatch=96.58,AligLength=409,E-val=0.0
+TTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTTCTGGCTGCA
+GTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTGTCCTGCAAT
+GTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCATCTCCAGTA
+GTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCTCCAACTTTA
+TCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTAACGACGGCT
+TGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATCCGAACTACT
+TTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTTTAAGAG
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_3/7_Confidence_0.286_Length_395_hit1_IdMatch=97.97,AligLength=395,E-val=0.0
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_29_Transcript_1/1_Confidence_0.000_Length_607_hit1_IdMatch=97.7,AligLength=608,E-val=0.0
+ACGCCCGAGAGCGTGGTCTTGGGCATGGCACTGTAGGCGACCTGACTCCCAGACTTTCGA
+GGGCGATTTCGCCCTCTTCGACGGGGTCCTTGAACCATTGAGCAATTCTTTCCCACAATT
+TGACGAGAAGATACACTCTGTACGGTAACCTTGGGGGAACGACGGTTTCTGGTGGAAAGA
+TTGTTTCCACTGTTGTTTGATATGCGCTTTGTAGTTGTGACGATGGTGGCCATGGCATAA
+TATTTACAAATTGTATTCTTGATTTGAGTTTGGGTTGTTTGATGTTATAGGGTCGGCAAG
+AGCTTACTTGCAGTTCTCTTCCTCTTTTTGCGGTCGAGAGTCTTTTTGTTGAGTCTCGTC
+CTTTGTTCTGCGGTCAGCAGTGATCTCTTCGATGCTACTTTAGGAGGTGGAAACCGGGAG
+AATAAGTCTTGAATTCTCACACGGTAGTCATCAGGATTTTTATGACTAACCTCTCTAATA
+AGCATCTGCACCTGGCGGGGACAGTGCCCCGGGAATTGCTGCATTATACTGTGAAACAGC
+TCCAAATCCAGGGTTTCATGAACGGGCACAATCTGTGGCACAGCTTTAGGGGCAGTTGCA
+TATTCAA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_1/2_Confidence_0.667_Length_236_hit1_IdMatch=98.73,AligLength=236,E-val=2e-113
+ATAGAAGCACTGTGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTG
+CCTATCTCCAGGAGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTC
+TCCATGAGTCGGAAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTG
+ACACTAAGAAAGTTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_27_Transcript_1/1_Confidence_0.000_Length_471_hit1_IdMatch=97.66,AligLength=471,E-val=0.0
+GCAAAAAGAATGCCTCTGATAGGGCAATCATAAAACTGTTAAACAAATACATGCCTAGGA
+CAGGAAATAAGAACTGGCCTGGTGTCCATACAACCCCGGAAGAAGGCATACTTGATGGTA
+TTAAGATAACGGCCAAATCCAGTGCAGGCGCTCCCTATTGGAGACACAAGGGGGAATGCC
+TAGACCATATAATTGATACTGGACTTCCTGTTGTGCTAAAGCATATAAAGGAAGGAACCC
+TCAATCAGTTGTGGCGGGAAAACCCTGAGATGTTCCTCGTTGAAGTTAAGAACAAACTTG
+ATAGATACGAGGTTTCGAAGCTTAAAGAGAAGACTAGACCCTATGTGTGTGTACCTGCGC
+ACTGGGCTCTCCTATTCTCGTGCTTGACTCAAGGATTCCAAGAAGGACTTCAAGTTTTTA
+GTAACTTGGACCCCAGTACAGAATGCTCGAATGCATATGGATTTTCATCCA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_2/7_Confidence_0.143_Length_224_hit1_IdMatch=97.77,AligLength=224,E-val=3e-104
+ACATCCTGGGTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTT
+GGCCGTACCTCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGG
+ACATATGCCATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGAT
+ACTCCTGCAACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_2/2_Confidence_0.333_Length_515_hit1_IdMatch=97.28,AligLength=515,E-val=0.0
+TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+GATGAAGAGACAAGGCTTGGTTGTCAAAGAGGGAA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_14_Transcript_1/1_Confidence_0.000_Length_210_hit1_IdMatch=98.1,AligLength=210,E-val=3e-98
+TGTCCCGTTGCACCCCCCATCCATTAACAATCGGGGTGGGCATACTCATGTCACTCGCCA
+GATGGGCGGAGTACCTCACCCTCCTCTTGGTCTAATACCCATAGCTCAGAAGTACGGGGT
+AGAGATCTTGGACCAGAAACATGTCTACACAGGAGGCACTTGGGATGGCTTTCTTAATAG
+ACTCGCCCAACAGATGGGCCGGACAACGGT
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_1/7_Confidence_0.286_Length_199_hit1_IdMatch=98.48,AligLength=197,E-val=2e-92
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGC
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_1/2_Confidence_0.667_Length_506_hit1_IdMatch=97.04,AligLength=506,E-val=0.0
+TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+GATGAAGAGACAAGGCTTAGTTGTCA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_2/2_Confidence_0.000_Length_284_hit1_IdMatch=98.94,AligLength=284,E-val=2e-139
+AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG
+TGAATCAGGTTTATGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
+AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
+AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
+TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_2/2_Confidence_0.333_Length_251_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118
+TGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCACC
+GAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACAAT
+TTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTCGT
+TCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCAAC
+AGTTCTTGTTA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_7/7_Confidence_0.000_Length_627_hit1_IdMatch=97.93,AligLength=627,E-val=0.0
+GTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCCTCAAACACTTTGTACTCATCATTCA
+GATTCGCCTCAGGAGGAGGAGGGCATCCTACAACCTCCTTGACATCATAGTCGTTGGATT
+GGACTGTCAAATTTATCTGCCTCACAGCCACTCTCTGCTCCCTCTTAAACTCGTCCAGGA
+ATCCTGACAATGTGGGGAACAGATTAATCCATCCCGCTTTGTCATCCTCTCCATCTGAAT
+AGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCTGACGAATCTGGATATTCAAAGTCCT
+GGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGCTCTTGCGTTTGCATGACAATAATCT
+CGCCGGGGATTGTGTTAACCACAGCGTGTATTGTCTCTTCGATCCGAGGTATGCTGAATC
+CCATTGTTATCATTAAACCCCTCATACGGTCATACAGAGTTCTTTGGCGTGCCGTTCTAG
+ATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAGAGCATCATCTCAAGAGCATCGCTCT
+CAGGCATTGTGGGGACATGTATCACACGGTGTCTGTGGTACACTCCCATAATTTGTACGC
+CAAGAAATTTGTGGTCCGTAATTAGAC
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_24_Transcript_1/1_Confidence_0.000_Length_280_hit1_IdMatch=96.79,AligLength=280,E-val=4e-129
+ACCATTTGTCCCCCATGGTGCATTTTCATGGTAAGGTAGTCACTGTTCCAGGAACCATCT
+GAGGTGGTAAAAAGGTCCTGGAAACCAGTATCTGGAGTGATATCCTCGTCAATGGAGACA
+GCTCCTAATTCAGCACCTTCAAACTCAATCACCCATTCGAGTGTGACAGTGAAGGTGGTG
+CTTCCTGTGTATCCACCGGTGGTAGAGGCAACAACCACATTGATGAAGCCATGATTGGCG
+TCATCAGGGTTGCCTTTGGTGAGATACCACTTACGGGTGG
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_6/7_Confidence_0.143_Length_1372_hit1_IdMatch=97.59,AligLength=1372,E-val=0.0
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
+CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
+TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
+TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
+CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
+ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
+CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
+TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
+TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
+TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
+GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
+GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
+TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
+TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
+AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
+AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
+TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_22_Transcript_1/1_Confidence_0.000_Length_289_hit1_IdMatch=95.5,AligLength=289,E-val=1e-128
+GGCCTGCAGGCCATAACTCGGTTGAGGTTTTGAGTGTCATTGCCTGAGATATTGTTGGCG
+GGGTCTGGAGACCATCCTATGGCAAGGGATCCAAAAGTATTTGCACTTCCAGATCCCACT
+ACCAGCACTCGGAGTTTCTTGGGTCGCCAGCGGGAATATAGCTTACTCTGCTGCTGAAGC
+CTAGAATCACTCATAGCCGTTGGACATATGGCTTGAGCAAAAAGGCTAGCTCCCACTGCG
+CGCTGCGGTTGTACCTCAATAACGCCTATAATGTCCACGCCCGAGAGCG
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_5/7_Confidence_0.286_Length_421_hit1_IdMatch=96.67,AligLength=421,E-val=0.0
+TACTCCTGCAACGTCCAGATTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAA
+AGCTGACGTTCTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTC
+TCTTTGACTGTCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTC
+TCCAAGTTCATCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTA
+GGCACTAGCTCCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGT
+AAGCCATCTAACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACT
+TTCTGTGATCCGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGG
+T
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_1/2_Confidence_0.667_Length_253_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118
+TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
+CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
+ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
+GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
+ACAGTTCTTGTTA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_20_Transcript_1/1_Confidence_0.000_Length_352_hit1_IdMatch=98.01,AligLength=352,E-val=8e-171
+GCATTCACTGCTCTAAGTTGCTCGGTCAGCTGGTCAATGCGGCGAAGTAGATTAGTTTCG
+ACAGTCTGAACTGCTTCATCAGCCACCCTAAATTTAGGGATGGGAGGGCTAATGACAGGA
+CCTTGGGTGTAATACTTGAGACATTTGCCAGTATCTCCAGTGCGGATATAATCTTTTGCA
+TCTGTGTAACTGGCAAACATAACAAAACCTGGGATAGAGTAACCTTGTATAACTGCAAAG
+AAGTTTGCTGTCTTCAAGGTCGTCTTGTCCTCAAGGTAGTAGGTTACATTTGTCCCTGGT
+GCATTTGTATACACATAAGCCTGGTGGGCAGCCGAAAAGGGGACCATTTGTC
diff -r 000000000000 -r d76a0d8a9eac test-data/singlets.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/singlets.fa	Sat Sep 02 07:09:11 2017 -0400
@@ -0,0 +1,45 @@
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_29_Transcript_1/1_Confidence_0.000_Length_607_hit1_IdMatch=97.7,AligLength=608,E-val=0.0
+ACGCCCGAGAGCGTGGTCTTGGGCATGGCACTGTAGGCGACCTGACTCCCAGACTTTCGA
+GGGCGATTTCGCCCTCTTCGACGGGGTCCTTGAACCATTGAGCAATTCTTTCCCACAATT
+TGACGAGAAGATACACTCTGTACGGTAACCTTGGGGGAACGACGGTTTCTGGTGGAAAGA
+TTGTTTCCACTGTTGTTTGATATGCGCTTTGTAGTTGTGACGATGGTGGCCATGGCATAA
+TATTTACAAATTGTATTCTTGATTTGAGTTTGGGTTGTTTGATGTTATAGGGTCGGCAAG
+AGCTTACTTGCAGTTCTCTTCCTCTTTTTGCGGTCGAGAGTCTTTTTGTTGAGTCTCGTC
+CTTTGTTCTGCGGTCAGCAGTGATCTCTTCGATGCTACTTTAGGAGGTGGAAACCGGGAG
+AATAAGTCTTGAATTCTCACACGGTAGTCATCAGGATTTTTATGACTAACCTCTCTAATA
+AGCATCTGCACCTGGCGGGGACAGTGCCCCGGGAATTGCTGCATTATACTGTGAAACAGC
+TCCAAATCCAGGGTTTCATGAACGGGCACAATCTGTGGCACAGCTTTAGGGGCAGTTGCA
+TATTCAA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_27_Transcript_1/1_Confidence_0.000_Length_471_hit1_IdMatch=97.66,AligLength=471,E-val=0.0
+GCAAAAAGAATGCCTCTGATAGGGCAATCATAAAACTGTTAAACAAATACATGCCTAGGA
+CAGGAAATAAGAACTGGCCTGGTGTCCATACAACCCCGGAAGAAGGCATACTTGATGGTA
+TTAAGATAACGGCCAAATCCAGTGCAGGCGCTCCCTATTGGAGACACAAGGGGGAATGCC
+TAGACCATATAATTGATACTGGACTTCCTGTTGTGCTAAAGCATATAAAGGAAGGAACCC
+TCAATCAGTTGTGGCGGGAAAACCCTGAGATGTTCCTCGTTGAAGTTAAGAACAAACTTG
+ATAGATACGAGGTTTCGAAGCTTAAAGAGAAGACTAGACCCTATGTGTGTGTACCTGCGC
+ACTGGGCTCTCCTATTCTCGTGCTTGACTCAAGGATTCCAAGAAGGACTTCAAGTTTTTA
+GTAACTTGGACCCCAGTACAGAATGCTCGAATGCATATGGATTTTCATCCA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_14_Transcript_1/1_Confidence_0.000_Length_210_hit1_IdMatch=98.1,AligLength=210,E-val=3e-98
+TGTCCCGTTGCACCCCCCATCCATTAACAATCGGGGTGGGCATACTCATGTCACTCGCCA
+GATGGGCGGAGTACCTCACCCTCCTCTTGGTCTAATACCCATAGCTCAGAAGTACGGGGT
+AGAGATCTTGGACCAGAAACATGTCTACACAGGAGGCACTTGGGATGGCTTTCTTAATAG
+ACTCGCCCAACAGATGGGCCGGACAACGGT
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_24_Transcript_1/1_Confidence_0.000_Length_280_hit1_IdMatch=96.79,AligLength=280,E-val=4e-129
+ACCATTTGTCCCCCATGGTGCATTTTCATGGTAAGGTAGTCACTGTTCCAGGAACCATCT
+GAGGTGGTAAAAAGGTCCTGGAAACCAGTATCTGGAGTGATATCCTCGTCAATGGAGACA
+GCTCCTAATTCAGCACCTTCAAACTCAATCACCCATTCGAGTGTGACAGTGAAGGTGGTG
+CTTCCTGTGTATCCACCGGTGGTAGAGGCAACAACCACATTGATGAAGCCATGATTGGCG
+TCATCAGGGTTGCCTTTGGTGAGATACCACTTACGGGTGG
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_22_Transcript_1/1_Confidence_0.000_Length_289_hit1_IdMatch=95.5,AligLength=289,E-val=1e-128
+GGCCTGCAGGCCATAACTCGGTTGAGGTTTTGAGTGTCATTGCCTGAGATATTGTTGGCG
+GGGTCTGGAGACCATCCTATGGCAAGGGATCCAAAAGTATTTGCACTTCCAGATCCCACT
+ACCAGCACTCGGAGTTTCTTGGGTCGCCAGCGGGAATATAGCTTACTCTGCTGCTGAAGC
+CTAGAATCACTCATAGCCGTTGGACATATGGCTTGAGCAAAAAGGCTAGCTCCCACTGCG
+CGCTGCGGTTGTACCTCAATAACGCCTATAATGTCCACGCCCGAGAGCG
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_20_Transcript_1/1_Confidence_0.000_Length_352_hit1_IdMatch=98.01,AligLength=352,E-val=8e-171
+GCATTCACTGCTCTAAGTTGCTCGGTCAGCTGGTCAATGCGGCGAAGTAGATTAGTTTCG
+ACAGTCTGAACTGCTTCATCAGCCACCCTAAATTTAGGGATGGGAGGGCTAATGACAGGA
+CCTTGGGTGTAATACTTGAGACATTTGCCAGTATCTCCAGTGCGGATATAATCTTTTGCA
+TCTGTGTAACTGGCAAACATAACAAAACCTGGGATAGAGTAACCTTGTATAACTGCAAAG
+AAGTTTGCTGTCTTCAAGGTCGTCTTGTCCTCAAGGTAGTAGGTTACATTTGTCCCTGGT
+GCATTTGTATACACATAAGCCTGGTGGGCAGCCGAAAAGGGGACCATTTGTC